I suggest you ...

Add option to show messages found in header file only once

Consider this: a.h contains 10 problems and is included in 10 modules.
That leaves you with 100 lint messages in the log, when in reality there are only 10 problems to fix.
So, having an option that shows messages in header files only the first time it is included would be really cool (and more honest in terms of MISRA violations).